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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ), 'gf_id' => 'HOM05D001423', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001423' ), 'data_identifier' => 'HOM05D001423', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001423', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '441', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10630' => 'bna', 'A03p19910' => 'bna', 'A04p27580' => 'bna', 'A05p09810' => 'bna', 'A08p05400' => 'bna', 'A10p18570' => 'bna', 'Aa31LG1G13290' => 'aar', 'Aa31LG5G21150' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5104' => 'aag', 'Actinidia03900' => 'ach', 'Actinidia03901' => 'ach', 'Actinidia04009' => 'ach', 'Actinidia07270' => 'ach', 'Actinidia16980' => 'ach', 'Actinidia24238' => 'ach', 'Actinidia24239' => 'ach', 'Actinidia32055' => 'ach', 'Ah.08g223730' => 'amhyb', 'Ah.08g223800' => 'amhyb', 'Ah.15g099990' => 'amhyb', 'Ah.15g100000' => 'amhyb', 'AL1G54310' => 'aly', 'AL4G32110' => 'aly', 'AL6G33220' => 'aly', 'AL970U10020' => 'aly', 'Aqoxy3G02873' => 'aox', 'Aqoxy4G02680' => 'aox', 'Aqoxy6G02305' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1J1N84' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4U64XY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.54F4RD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.D6GCTI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T7DLBP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U6ZQZC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJH38K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UUW3MN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V1GP0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y4QQE4' => 'arhy', 'AT1G47870' => 'ath', 'AT2G36010' => 'ath', 'AT5G22220' => 'ath', 'ATR0772G011' => 'atr', 'ATR0933G003' => 'atr', 'Atru.chr13.306' => 'acertr', 'Atru.chr3.3142' => 'acertr', 'Atru.chr8.1394' => 'acertr', 'AUR62001537' => 'cqu', 'AUR62001538' => 'cqu', 'AUR62020244' => 'cqu', 'AUR62020245' => 'cqu', 'BcaB01g03862' => 'bca', 'BcaB01g04721' => 'bca', 'BcaB02g09391' => 'bca', 'BcaB04g17476' => 'bca', 'BcaB06g28907' => 'bca', 'BcaB08g36447' => 'bca', 'BcaC01g05677' => 'bca', 'BcaC01g06597' => 'bca', 'BcaC02g07639' => 'bca', 'BcaC02g11702' => 'bca', 'BcaC04g19559' => 'bca', 'BcaC07g37188' => 'bca', 'BolC3t13697H' => 'bol', 'BolC3t14731H' => 'bol', 'BolC4t22861H' => 'bol', 'BolC4t27986H' => 'bol', 'BolC8t47422H' => 'bol', 'BolC9t58311H' => 'bol', 'BraA03t10375Z' => 'bra', 'BraA03t11242Z' => 'bra', 'BraA04t18253Z' => 'bra', 'BraA05t19933Z' => 'bra', 'BraA08t32544Z' => 'bra', 'BraA10t43937Z' => 'bra', 'C03p12240' => 'bna', 'C03p23310' => 'bna', 'C04p12170' => 'bna', 'C04p65080' => 'bna', 'C08p05840' => 'bna', 'C09p54420' => 'bna', 'CAN.G1463.7' => 'can', 'CAN.G22.26' => 'can', 'CAN.G311.20' => 'can', 'CAN.G574.34' => 'can', 'CAN.G745.32' => 'can', 'CANSAT54G1815' => 'cansat', 'CANSAT64G1345' => 'cansat', 'CARHR037470' => 'chi', 'CARHR130270' => 'chi', 'CARHR191330' => 'chi', 'Carub.0001s3698' => 'cru', 'Carub.0004s1776' => 'cru', 'Carub.0006s1996' => 'cru', 'Ca_11718_v3' => 'car', 'Ca_15485_v3' => 'car', 'Ca_19459_v3' => 'car', 'Ca_29923_v3' => 'car', 'CBR_g54574' => 'cbr', 'Cc00_g32910' => 'ccan', 'Cc00_g35310' => 'ccan', 'Cc01_g08610' => 'ccan', 'Cc04_g14590' => 'ccan', 'Cc06_g06370' => 'ccan', 'Cc10_g01770' => 'ccan', 'Cc11_g04370' => 'ccan', 'CDE02G1876' => 'cde', 'CDE02G2694' => 'cde', 'CDE08G0261' => 'cde', 'CDE08G1029' => 'cde', 'CDE11G1262' => 'cde', 'Cfa009968' => 'cfa', 'Cfa016670' => 'cfa', 'Ciclev10001165m.g' => 'ccl', 'Ciclev10011632m.g' => 'ccl', 'Ciclev10028409m.g' => 'ccl', 'CiPaw.07G151100' => 'cil', 'CiPaw.09G019100' => 'cil', 'CiPaw.10G015500' => 'cil', 'CiPaw.13G131500' => 'cil', 'CiPaw.13G131600' => 'cil', 'ClCG02G022380' => 'cla', 'ClCG04G010370' => 'cla', 'ClCG08G014380' => 'cla', 'COL.COLO4_22655' => 'col', 'COL.COLO4_29612' => 'col', 'Cpa.g.c39412' => 'cpa', 'Cpa.g.sc104.59' => 'cpa', 'Cpa.g.sc195.40' => 'cpa', 'Cre01.g052300' => 'cre', 'CsaV3_2G029450' => 'csa', 'CsaV3_6G038510' => 'csa', 'CsaV3_6G041000' => 'csa', 'CsaV3_7G027730' => 'csa', 'CSS0008429' => 'camsi', 'CSS0009558' => 'camsi', 'CSS0014737' => 'camsi', 'CSS0020105' => 'camsi', 'CSS0025781' => 'camsi', 'CSS0036628' => 'camsi', 'CSS0041866' => 'camsi', 'CSS0042107' => 'camsi', 'DCAR_006178' => 'dca', 'DCAR_010316' => 'dca', 'DCAR_013863' => 'dca', 'DCAR_020719' => 'dca', 'Dinv08129' => 'din', 'Dinv12323' => 'din', 'Dinv17084' => 'din', 'Dinv31746' => 'din', 'Dinv31835' => 'din', 'Duzib041G0322' => 'dzi', 'Duzib093G1221' => 'dzi', 'Duzib093G1515' => 'dzi', 'Duzib106G1077' => 'dzi', 'Duzib128G0810' => 'dzi', 'Duzib150G0449' => 'dzi', 'Duzib168G1069' => 'dzi', 'Duzib170G0364' => 'dzi', 'ECA233G2821' => 'eca', 'ECA238G0159' => 'eca', 'ECA238G2343' => 'eca', 'ECA238G3851' => 'eca', 'EL10Ac7g16319' => 'bvu', 'Eucgr.A02602' => 'egr', 'Eucgr.J00539' => 'egr', 'FAN02G3843' => 'fan', 'FAN04G0659' => 'fan', 'FAN05G1363' => 'fan', 'FAN05G1580' => 'fan', 'FAN09G4848' => 'fan', 'FAN10G0283' => 'fan', 'FAN11G1515' => 'fan', 'FAN14G5667' => 'fan', 'FAN15G1891' => 'fan', 'FAN16G3660' => 'fan', 'FAN20G1632' => 'fan', 'FAN21G3546' => 'fan', 'FAN25G1475' => 'fan', 'FAN25G1974' => 'fan', 'FAN27G0518' => 'fan', 'FAN27G2868' => 'fan', 'FvH4_2g38580' => 'fve', 'FvH4_3g25990' => 'fve', 'FvH4_6g19970' => 'fve', 'Glyma.02G198700' => 'gma', 'Glyma.04G024800' => 'gma', 'Glyma.06G024900' => 'gma', 'Glyma.10G078200' => 'gma', 'Glyma.11G180100' => 'gma', 'Glyma.12G093400' => 'gma', 'Gohir.A01G137695' => 'ghi', 'Gohir.A07G112100' => 'ghi', 'Gohir.A09G097800' => 'ghi', 'Gohir.A11G316150' => 'ghi', 'Gohir.A13G222042' => 'ghi', 'Gohir.A13G222184' => 'ghi', 'Gohir.D01G126700' => 'ghi', 'Gohir.D07G115600' => 'ghi', 'Gohir.D09G097600' => 'ghi', 'Gohir.D11G333150' => 'ghi', 'Gohir.D11G333550' => 'ghi', 'Gohir.D11G335600' => 'ghi', 'Gohir.D11G336300' => 'ghi', 'Gohir.D11G336600' => 'ghi', 'Gohir.D13G223800' => 'ghi', 'Gohir.D13G226150' => 'ghi', 'Gohir.D13G226800' => 'ghi', 'Gohir.D13G227125' => 'ghi', 'Gorai.001G123900' => 'gra', 'Gorai.002G157200' => 'gra', 'Gorai.006G114300' => 'gra', 'Gorai.007G364600' => 'gra', 'Gorai.007G366000' => 'gra', 'Gorai.007G366400' => 'gra', 'Gorai.007G366600' => 'gra', 'Gorai.010G046300' => 'gra', 'Gorai.013G257100' => 'gra', 'GSVIVG01009890001' => 'vvi', 'GSVIVG01033931001' => 'vvi', 'GSVIVG01036059001' => 'vvi', 'HanXRQChr02g0053781' => 'han', 'HanXRQChr04g0106741' => 'han', 'HanXRQChr11g0322981' => 'han', 'HanXRQChr13g0398231' => 'han', 'HanXRQChr14g0433131' => 'han', 'Haze_19682' => 'cav', 'Haze_19683' => 'cav', 'Haze_22623' => 'cav', 'Haze_23329' => 'cav', 'Hma1.2p1_0793F.1_g218660' => 'hma', 'Hma1.2p1_1442F.1_g283780' => 'hma', 'HPP92_001988' => 'vpl', 'HPP92_007136' => 'vpl', 'HPP92_023071' => 'vpl', 'HPP92_023072' => 'vpl', 'HPP92_025366' => 'vpl', 'Hund18791' => 'sun', 'Hund20942' => 'sun', 'Lalb_Chr01g0004971' => 'lal', 'Lalb_Chr01g0017891' => 'lal', 'Lalb_Chr03g0028341' => 'lal', 'Lalb_Chr08g0246151' => 'lal', 'Lalb_Chr19g0136301' => 'lal', 'Lalb_Chr19g0136311' => 'lal', 'Lalb_Chr25g0288081' => 'lal', 'Lj1A1045G47' => 'lonja', 'Lj1A1046T48' => 'lonja', 'Lj1A1047T39' => 'lonja', 'Lj1A1047T40' => 'lonja', 'Lj1A261G28' => 'lonja', 'Lj1C1045G6' => 'lonja', 'Lj1g0017570' => 'lja', 'Lj3g0011053' => 'lja', 'Lj3g0021599' => 'lja', 'Lj5g0016133' => 'lja', 'Lsat_1_v5_gn_2_35961' => 'lsa', 'Lsat_1_v5_gn_2_55341' => 'lsa', 'Lsat_1_v5_gn_3_28400' => 'lsa', 'Lsat_1_v5_gn_6_35080' => 'lsa', 'Manes.04G000400' => 'mes', 'Manes.08G031600' => 'mes', 'Manes.11G165300' => 'mes', 'Manes.18G014400' => 'mes', 'Mapoly0113s0037' => 'mpo', 'MBI01_g17600_MAGBIO' => 'mbi', 'MBI05_g15347_MAGBIO' => 'mbi', 'MBI17_g18934_MAGBIO' => 'mbi', 'MCO01G410' => 'mco', 'MD03G1152700' => 'mdo', 'MD08G1013800' => 'mdo', 'MD11G1172700' => 'mdo', 'MD12G1037100' => 'mdo', 'MD14G1036100' => 'mdo', 'Medtr1g105110' => 'mtr', 'Medtr3g113800' => 'mtr', 'Medtr4g052000' => 'mtr', 'MELO3C011003.2' => 'cme', 'MELO3C014514.2' => 'cme', 'MELO3C024578.2' => 'cme', 'MELO3C033132.2' => 'cme', 'Migut.C00805' => 'egut', 'Migut.J00719' => 'egut', 'Migut.N02463' => 'egut', 'MSTRG.12382' => 'ama', 'MSTRG.17687' => 'ama', 'MSTRG.18784' => 'ama', 'MSTRG.5907' => 'ama', 'Nitab4.5_0000020g0310' => 'nta', 'Nitab4.5_0000380g0210' => 'nta', 'Nitab4.5_0000893g0030' => 'nta', 'Nitab4.5_0001135g0200' => 'nta', 'Nitab4.5_0001540g0040' => 'nta', 'Nitab4.5_0002706g0020' => 'nta', 'Nitab4.5_0007138g0010' => 'nta', 'Nn2g14264' => 'nnu', 'Nn5g29335' => 'nnu', 'Nn6g34753' => 'nnu', 'Oeu009054.1' => 'oeu', 'Oeu020153.1' => 'oeu', 'Oeu037545.1' => 'oeu', 'Oeu039620.1' => 'oeu', 'Oeu042175.1' => 'oeu', 'Oeu051598.2' => 'oeu', 'Oeu064180.2' => 'oeu', 'Os02g0537500' => 'osa', 'Os04g0112200' => 'osa', 'Os04g0416100' => 'osa', 'Os12g0158800' => 'osa', 'Peaxi162Scf00029g00007' => 'pax', 'Peaxi162Scf00224g00820' => 'pax', 'Peaxi162Scf00438g00628' => 'pax', 'Peaxi162Scf00755g00019' => 'pax', 'PGR004G2461' => 'pgr', 'PGR102G0925' => 'pgr', 'PGR102G1471' => 'pgr', 'PGR119G0771' => 'pgr', 'PGSC0003DMG400003778' => 'stu', 'PGSC0003DMG400016418' => 'stu', 'PGSC0003DMG400019629' => 'stu', 'PGSC0003DMG401005482' => 'stu', 'PGSC0003DMG401005932' => 'stu', 'PGSC0003DMG402005932' => 'stu', 'Phvul.007G269500' => 'pvu', 'Phvul.009G016300' => 'pvu', 'Phvul.011G097700' => 'pvu', 'Potri.002G023400' => 'ptr', 'Potri.004G200800' => 'ptr', 'Potri.006G205100' => 'ptr', 'Potri.009G161900' => 'ptr', 'Potri.016G072300' => 'ptr', 'Pp3c11_6020' => 'ppa', 'Pp3c1_6880' => 'ppa', 'Pp3c2_30010' => 'ppa', 'Pp3c7_25430' => 'ppa', 'PRCOL_00001191' => 'pco', 'Prupe.1G366800' => 'ppe', 'Prupe.6G139100' => 'ppe', 'Prupe.6G139900' => 'ppe', 'Prupe.7G098100' => 'ppe', 'Psat5g013280' => 'psa', 'Psat6g083240' => 'psa', 'Psat7g187080' => 'psa', 'PSO339G3478' => 'pso', 'PSO384G4180' => 'pso', 'PSO541G2575' => 'pso', 'PSO675G9036' => 'pso', 'QL01p011359' => 'qlo', 'QL01p011622' => 'qlo', 'QL02p011415' => 'qlo', 'QL07p037461' => 'qlo', 'RcHm_v2.0_Chr3g0475421' => 'rch', 'RcHm_v2.0_Chr5g0047281' => 'rch', 'RcHm_v2.0_Chr6g0302711' => 'rch', 'Rhsim01G0202000' => 'rsi', 'Rhsim03G0066900' => 'rsi', 'Rhsim06G0022000' => 'rsi', 'Sabra04G0135900' => 'sbr', 'Sabra05G0184000' => 'sbr', 'Sabra06G0158100' => 'sbr', 'Sabra09G0126600' => 'sbr', 'Sabra16G0075200' => 'sbr', 'SalBow1G5196' => 'sbo', 'SalBow6G4159' => 'sbo', 'SalBow7G4306' => 'sbo', 'Sc12g0004780' => 'sci', 'Sc21g0006880' => 'sci', 'Sed0004897' => 'sed', 'Sed0009146' => 'sed', 'Sed0010210' => 'sed', 'SEGI_06483' => 'sgi', 'SEGI_06640' => 'sgi', 'SEGI_10860' => 'sgi', 'SEGI_19642' => 'sgi', 'SEGI_21870' => 'sgi', 'SGA_v2.0_scaffold114G31958' => 'sas', 'SGA_v2.0_scaffold11G05912' => 'sas', 'SGA_v2.0_scaffold177G39470' => 'sas', 'SGA_v2.0_scaffold295G47494' => 'sas', 'SGA_v2.0_scaffold7G03982' => 'sas', 'SHI12300' => 'shi', 'SMO133G0001' => 'smo', 'SMO228G0135' => 'smo', 'Solyc01g007760.3' => 'sly', 'Solyc04g081350.3' => 'sly', 'Solyc06g074010.3' => 'sly', 'Solyc11g068800.2' => 'sly', 'Sopen01g003300' => 'spe', 'Sopen04g034970' => 'spe', 'Sopen06g030420' => 'spe', 'Sopen06g030430' => 'spe', 'Sopen11g027520' => 'spe', 'Sp1g34840' => 'spa', 'Sp4g18270' => 'spa', 'Sp6g23010' => 'spa', 'TAR268G0001' => 'tar', 'TAR365G0063' => 'tar', 'TAR365G0412' => 'tar', 'TAR376G0023' => 'tar', 'TAR623G1036' => 'tar', 'TAR633G0387' => 'tar', 'TAR636G3453' => 'tar', 'THA.LOC104799561' => 'tha', 'THA.LOC104799748' => 'tha', 'THA.LOC104804483' => 'tha', 'THA.LOC104807108' => 'tha', 'THA.LOC104810932' => 'tha', 'THA.LOC104813196' => 'tha', 'THA.LOC104826440' => 'tha', 'Thecc.05G101100' => 'tca', 'Thecc.08G043000' => 'tca', 'Thecc.08G043200' => 'tca', 'Thecc.09G275800' => 'tca', 'Thhalv10011567m.g' => 'esa', 'Thhalv10015215m.g' => 'esa', 'Thhalv10015650m.g' => 'esa', 'Thhalv10016580m.g' => 'esa', 'TPR.G23561' => 'tpr', 'TPR.G34547' => 'tpr', 'TPR.G4664' => 'tpr', 'TWI31G1092' => 'twi', 'TWI53G0346' => 'twi', 'TWI56G0944' => 'twi', 'TWI74G0760' => 'twi', 'TWI79G1010' => 'twi', 'unitig_27.g25122' => 'ugi', 'unitig_699.g19453' => 'ugi', 'unitig_748.g7770' => 'ugi', 'unitig_8.g4299' => 'ugi', 'vmacro07462' => 'vma', 'vmacro14326' => 'vma', 'VMungo0720G1943' => 'vmu', 'VMungo1127G1029' => 'vmu', 'VMungo1127G2282' => 'vmu', 'VMungo1309G0766' => 'vmu', 'Zm00001eb083590' => 'zma', 'Zm00001eb089380' => 'zma', 'Zm00001eb181510' => 'zma', 'Zm00001eb243000' => 'zma', 'Zm00001eb292470' => 'zma', 'Zm00001eb389000' => 'zma', 'Zm00001eb407120' => 'zma' ) $gf_id = 'HOM05D001423' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001423' ) $data_identifier = 'HOM05D001423' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 4, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 10, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 12, 'bol' => (int) 6, 'bra' => (int) 6, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 7, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 8, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 16, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 2, 'vpl' => (int) 5, 'sun' => (int) 2, 'lal' => (int) 7, 'lonja' => (int) 6, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 7, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 7, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 4, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb407120' $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